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revision 1.4, Mon Oct 2 03:15:37 2006 UTC revision 1.30, Thu Apr 19 00:05:51 2007 UTC
# Line 88  Line 88 
88  TRUE if this is a feature-filtered search, else FALSE. B<NOTE> that this  TRUE if this is a feature-filtered search, else FALSE. B<NOTE> that this
89  field is updated by the B<FeatureQuery> object.  field is updated by the B<FeatureQuery> object.
90    
91    =item extraPos
92    
93    Hash indicating which extra columns should be put at the end. Extra columns
94    not mentioned in this hash are put at the beginning. Use the L</SetExtraPos>
95    method to change this option.
96    
97  =back  =back
98    
99  =head2 Adding a new Search Tool  =head2 Adding a new Search Tool
# Line 113  Line 119 
119    
120  =item 4  =item 4
121    
122  In the C<SearchSkeleton.cgi> script, add a C<use> statement for your search tool  In the C<SearchSkeleton.cgi> script and add a C<use> statement for your search tool.
 and then put the class name in the C<@advancedClasses> list.  
123    
124  =back  =back
125    
# Line 177  Line 182 
182    
183  =back  =back
184    
185    If you are doing a feature search, you can also change the list of feature
186    columns displayed and their display order by overriding
187    L</DefaultFeatureColumns>.
188    
189  Finally, when generating the code for your controls, be sure to use any incoming  Finally, when generating the code for your controls, be sure to use any incoming
190  query parameters as default values so that the search request is persistent.  query parameters as default values so that the search request is persistent.
191    
# Line 214  Line 223 
223                      }                      }
224                  }                  }
225              }              }
         }  
226          # Close the session file.          # Close the session file.
227          $self->CloseSession();          $self->CloseSession();
228            }
229          # Return the result count.          # Return the result count.
230          return $retVal;          return $retVal;
231      }      }
232    
233  A Find method is of course much more complicated than generating a form, and there  A Find method is of course much more complicated than generating a form, and there
234  are variations on the above them. For example, you could eschew feature filtering  are variations on the above theme. For example, you could eschew feature filtering
235  entirely in favor of your own custom filtering, you could include extra columns  entirely in favor of your own custom filtering, you could include extra columns
236  in the output, or you could search for something that's not a feature at all. The  in the output, or you could search for something that's not a feature at all. The
237  above code is just a loose framework.  above code is just a loose framework.
238    
239    In addition to the finding and filtering, it is necessary to send status messages
240    to the output so that the user does not get bored waiting for results. The L</PrintLine>
241    method performs this function. The single parameter should be text to be
242    output to the browser. In general, you'll invoke it as follows.
243    
244        $self->PrintLine("...my message text...<br />");
245    
246    The break tag is optional. When the Find method gets control, a paragraph will
247    have been started so that everything is XHTML-compliant.
248    
249  If you wish to add your own extra columns to the output, use the B<AddExtraColumns>  If you wish to add your own extra columns to the output, use the B<AddExtraColumns>
250  method of the feature query object.  method of the feature query object.
251    
# Line 241  Line 260 
260    
261  # This counter is used to insure every form on the page has a unique name.  # This counter is used to insure every form on the page has a unique name.
262  my $formCount = 0;  my $formCount = 0;
263    # This counter is used to generate unique DIV IDs.
264    my $divCount = 0;
265    
266  =head2 Public Methods  =head2 Public Methods
267    
268  =head3 new  =head3 new
269    
270  C<< my $shelp = SearchHelper->new($query); >>  C<< my $shelp = SearchHelper->new($cgi); >>
271    
272  Construct a new SearchHelper object.  Construct a new SearchHelper object.
273    
274  =over 4  =over 4
275    
276  =item query  =item cgi
277    
278  The CGI query object for the current script.  The CGI query object for the current script.
279    
# Line 262  Line 283 
283    
284  sub new {  sub new {
285      # Get the parameters.      # Get the parameters.
286      my ($class, $query) = @_;      my ($class, $cgi) = @_;
287      # Check for a session ID.      # Check for a session ID.
288      my $session_id = $query->param("SessionID");      my $session_id = $cgi->param("SessionID");
289      my $type = "old";      my $type = "old";
290      if (! $session_id) {      if (! $session_id) {
291            Trace("No session ID found.") if T(3);
292          # Here we're starting a new session. We create the session ID and          # Here we're starting a new session. We create the session ID and
293          # store it in the query object.          # store it in the query object.
294          $session_id = NewSessionID();          $session_id = NewSessionID();
295          $type = "new";          $type = "new";
296          $query->param(-name => 'SessionID', -value => $session_id);          $cgi->param(-name => 'SessionID', -value => $session_id);
297        } else {
298            Trace("Session ID is $session_id.") if T(3);
299      }      }
300      # Compute the subclass name.      # Compute the subclass name.
301      $class =~ /SH(.+)$/;      my $subClass;
302      my $subClass = $1;      if ($class =~ /SH(.+)$/) {
303            # Here we have a real search class.
304            $subClass = $1;
305        } else {
306            # Here we have a bare class. The bare class cannot search, but it can
307            # process search results.
308            $subClass = 'SearchHelper';
309        }
310      # Insure everybody knows we're in Sprout mode.      # Insure everybody knows we're in Sprout mode.
311      $query->param(-name => 'SPROUT', -value => 1);      $cgi->param(-name => 'SPROUT', -value => 1);
312      # Generate the form name.      # Generate the form name.
313      my $formName = "$class$formCount";      my $formName = "$class$formCount";
314      $formCount++;      $formCount++;
# Line 285  Line 316 
316      # as well as an indicator as to whether or not the session is new, plus the      # as well as an indicator as to whether or not the session is new, plus the
317      # class name and a placeholder for the Sprout object.      # class name and a placeholder for the Sprout object.
318      my $retVal = {      my $retVal = {
319                    query => $query,                    query => $cgi,
320                    type => $type,                    type => $type,
321                    class => $subClass,                    class => $subClass,
322                    sprout => undef,                    sprout => undef,
# Line 295  Line 326 
326                    genomeList => undef,                    genomeList => undef,
327                    genomeParms => [],                    genomeParms => [],
328                    filtered => 0,                    filtered => 0,
329                      extraPos => {},
330                   };                   };
331      # Bless and return it.      # Bless and return it.
332      bless $retVal, $class;      bless $retVal, $class;
# Line 316  Line 348 
348      return $self->{query};      return $self->{query};
349  }  }
350    
351    
352    
353  =head3 DB  =head3 DB
354    
355  C<< my $sprout = $shelp->DB(); >>  C<< my $sprout = $shelp->DB(); >>
# Line 353  Line 387 
387      return ($self->{type} eq 'new');      return ($self->{type} eq 'new');
388  }  }
389    
390    =head3 SetExtraPos
391    
392    C<< $shelp->SetExtraPos(@columnMap); >>
393    
394    Indicate whether the extra columns should be in the front (C<0>) or end (C<1>) columns of the results.
395    
396    =over 4
397    
398    =item columnMap
399    
400    A list of extra columns to display at the end.
401    
402    =back
403    
404    =cut
405    
406    sub SetExtraPos {
407        # Get the parameters.
408        my ($self, @columnMap) = @_;
409        # Convert the column map to a hash.
410        my %map = map { $_ => 1 } @columnMap;
411        # Save a reference to it.
412        $self->{extraPos} = \%map;
413    }
414    
415  =head3 ID  =head3 ID
416    
417  C<< my $sessionID = $shelp->ID(); >>  C<< my $sessionID = $shelp->ID(); >>
# Line 447  Line 506 
506      my ($self, $title) = @_;      my ($self, $title) = @_;
507      # Get the CGI object.      # Get the CGI object.
508      my $cgi = $self->Q();      my $cgi = $self->Q();
509      # Start the form.      # Start the form. Note we use the override option on the Class value, in
510        # case the Advanced button was used.
511      my $retVal = "<div class=\"search\">\n" .      my $retVal = "<div class=\"search\">\n" .
512                   $cgi->start_form(-method => 'POST',                   $cgi->start_form(-method => 'POST',
513                                    -action => $cgi->url(-relative => 1),                                    -action => $cgi->url(-relative => 1),
514                                    -name => $self->FormName()) .                                    -name => $self->FormName()) .
515                   $cgi->hidden(-name => 'Class',                   $cgi->hidden(-name => 'Class',
516                                -value => $self->{class}) .                                -value => $self->{class},
517                                  -override => 1) .
518                   $cgi->hidden(-name => 'SPROUT',                   $cgi->hidden(-name => 'SPROUT',
519                                -value => 1) .                                -value => 1) .
520                   $cgi->h3($title);                   $cgi->h3($title);
# Line 607  Line 668 
668    
669  =head3 PutFeature  =head3 PutFeature
670    
671  C<< $shelp->PutFeature($fquery); >>  C<< $shelp->PutFeature($fdata); >>
672    
673  Store a feature in the result cache. This is the workhorse method for most  Store a feature in the result cache. This is the workhorse method for most
674  searches, since the primary data item in the database is features.  searches, since the primary data item in the database is features.
# Line 618  Line 679 
679  the feature query object using the B<AddExtraColumns> method. For example, the following  the feature query object using the B<AddExtraColumns> method. For example, the following
680  code adds columns for essentiality and virulence.  code adds columns for essentiality and virulence.
681    
682      $fq->AddExtraColumns(essential => $essentialFlag, virulence => $vfactor);      $fd->AddExtraColumns(essential => $essentialFlag, virulence => $vfactor);
683      $shelp->PutFeature($fq);      $shelp->PutFeature($fd);
684    
685  For correct results, all values should be specified for all extra columns in all calls to  For correct results, all values should be specified for all extra columns in all calls to
686  B<PutFeature>. (In particular, the column header names are computed on the first  B<PutFeature>. (In particular, the column header names are computed on the first
# Line 629  Line 690 
690      if (! $essentialFlag) {      if (! $essentialFlag) {
691          $essentialFlag = undef;          $essentialFlag = undef;
692      }      }
693      $fq->AddExtraColumns(essential => $essentialFlag, virulence => $vfactor);      $fd->AddExtraColumns(essential => $essentialFlag, virulence => $vfactor);
694      $shelp->PutFeature($fq);      $shelp->PutFeature($fd);
695    
696  =over 4  =over 4
697    
698  =item fquery  =item fdata
699    
700  FeatureQuery object containing the current feature data.  B<FeatureData> object containing the current feature data.
701    
702  =back  =back
703    
# Line 644  Line 705 
705    
706  sub PutFeature {  sub PutFeature {
707      # Get the parameters.      # Get the parameters.
708      my ($self, $fq) = @_;      my ($self, $fd) = @_;
709      # Get the CGI query object.      # Get the CGI query object.
710      my $cgi = $self->Q();      my $cgi = $self->Q();
711      # Get the feature data.      # Get the feature data.
712      my $record = $fq->Feature();      my $record = $fd->Feature();
713      my $extraCols = $fq->ExtraCols();      my $extraCols = $fd->ExtraCols();
714      # Check for a first-call situation.      # Check for a first-call situation.
715      if (! defined $self->{cols}) {      if (! defined $self->{cols}) {
716          # Here we need to set up the column information. Start with the defaults.          Trace("Setting up the columns.") if T(3);
717          $self->{cols} = $self->DefaultFeatureColumns();          # Tell the user what's happening.
718          # Add the externals if they were requested.          $self->PrintLine("Creating output columns.<br />");
719          if ($cgi->param('ShowAliases')) {          # Here we need to set up the column information. First we accumulate the extras,
720              push @{$self->{cols}}, 'alias';          # sorted by column name and separate by whether they go in the beginning or the
721          }          # end.
722          # Append the extras, sorted by column name.          my @xtraNamesFront = ();
723            my @xtraNamesEnd = ();
724            my $xtraPosMap = $self->{extraPos};
725          for my $col (sort keys %{$extraCols}) {          for my $col (sort keys %{$extraCols}) {
726              push @{$self->{cols}}, "X=$col";              if ($xtraPosMap->{$col}) {
727                    push @xtraNamesEnd, "X=$col";
728                } else {
729                    push @xtraNamesFront, "X=$col";
730          }          }
731          # Write out the column headers. This also prepares the cache file to receive          }
732            # Set up the column name array.
733            my @colNames = ();
734            # Put in the extra columns that go in the beginning.
735            push @colNames, @xtraNamesFront;
736            # Add the default columns.
737            push @colNames, $self->DefaultFeatureColumns();
738            # Add any additional columns requested by the feature filter.
739            push @colNames, FeatureQuery::AdditionalColumns($self);
740            # If extras go at the end, put them in here.
741            push @colNames, @xtraNamesEnd;
742            Trace("Full column list determined.") if T(3);
743            # Save the full list.
744            $self->{cols} = \@colNames;
745            # Write out the column names. This also prepares the cache file to receive
746          # output.          # output.
747          $self->WriteColumnHeaders(map { $self->FeatureColumnTitle($_) } @{$self->{cols}});          Trace("Writing column headers.") if T(3);
748            $self->WriteColumnHeaders(@{$self->{cols}});
749            Trace("Column headers written.") if T(3);
750      }      }
751      # Get the feature ID.      # Get the feature ID.
752      my ($fid) = $record->Value('Feature(id)');      my $fid = $fd->FID();
753      # Loop through the column headers, producing the desired data.      # Loop through the column headers, producing the desired data. The first column
754      my @output = ();      # is the feature ID. The feature ID does not show up in the output: its purpose
755        # is to help the various output formatters.
756        my @output = ($fid);
757      for my $colName (@{$self->{cols}}) {      for my $colName (@{$self->{cols}}) {
758          push @output, $self->FeatureColumnValue($colName, $record, $extraCols);          push @output, $self->FeatureColumnValue($colName, $record, $extraCols);
759      }      }
760      # Compute the sort key. The sort key floats NMPDR organism features to the      # Compute the sort key. The sort key usually floats NMPDR organism features to the
761      # top of the return list.      # top of the return list.
762      my $key = $self->SortKey($record);      my $key = $self->SortKey($fd);
763      # Write the feature data.      # Write the feature data.
764      $self->WriteColumnData($key, @output);      $self->WriteColumnData($key, @output);
765  }  }
# Line 756  Line 840 
840      # Check for an open session file.      # Check for an open session file.
841      if (defined $self->{fileHandle}) {      if (defined $self->{fileHandle}) {
842          # We found one, so close it.          # We found one, so close it.
843            Trace("Closing session file.") if T(2);
844          close $self->{fileHandle};          close $self->{fileHandle};
845            # Tell the user.
846            my $cgi = $self->Q();
847            $self->PrintLine("Output formatting complete.<br />");
848      }      }
849  }  }
850    
# Line 823  Line 911 
911                                                      ['Genome(genus)', 'Genome(species)',                                                      ['Genome(genus)', 'Genome(species)',
912                                                       'Genome(unique-characterization)',                                                       'Genome(unique-characterization)',
913                                                       'Genome(primary-group)']);                                                       'Genome(primary-group)']);
914          # Null out the supporting group.          # Format and cache the name and display group.
915          $group = "" if ($group eq $FIG_Config::otherGroup);          ($orgName, $group) = $self->SaveOrganismData($group, $genomeID, $genus, $species,
916          # If the organism does not exist, format an unknown name.                                                              $strain);
         if (! defined($genus)) {  
             $orgName = "Unknown Genome $genomeID";  
         } else {  
             # It does exist, so format the organism name.  
             $orgName = "$genus $species";  
             if ($strain) {  
                 $orgName .= " $strain";  
             }  
         }  
         # Save this organism in the cache.  
         $cache->{$genomeID} = [$orgName, $group];  
917      }      }
918      # Return the result.      # Return the result.
919      return ($orgName, $group);      return ($orgName, $group);
# Line 947  Line 1024 
1024    
1025  =head3 ComputeFASTA  =head3 ComputeFASTA
1026    
1027  C<< my $fasta = $shelp->ComputeFASTA($incomingType, $desiredType, $sequence); >>  C<< my $fasta = $shelp->ComputeFASTA($desiredType, $sequence); >>
1028    
1029  Parse a sequence input and convert it into a FASTA string of the desired type. Note  Parse a sequence input and convert it into a FASTA string of the desired type.
 that it is possible to convert a DNA sequence into a protein sequence, but the reverse  
 is not possible.  
1030    
1031  =over 4  =over 4
1032    
 =item incomingType  
   
 C<dna> if this is a DNA sequence, C<prot> if this is a protein sequence.  
   
1033  =item desiredType  =item desiredType
1034    
1035  C<dna> to return a DNA sequence, C<prot> to return a protein sequence. If the  C<dna> to return a DNA sequence, C<prot> to return a protein sequence.
 I<$incomingType> is C<prot> and this value is C<dna>, an error will be thrown.  
1036    
1037  =item sequence  =item sequence
1038    
# Line 984  Line 1054 
1054    
1055  sub ComputeFASTA {  sub ComputeFASTA {
1056      # Get the parameters.      # Get the parameters.
1057      my ($self, $incomingType, $desiredType, $sequence) = @_;      my ($self, $desiredType, $sequence) = @_;
1058      # Declare the return variable. If an error occurs, it will remain undefined.      # Declare the return variable. If an error occurs, it will remain undefined.
1059      my $retVal;      my $retVal;
1060        # This variable will be cleared if an error is detected.
1061        my $okFlag = 1;
1062      # Create variables to hold the FASTA label and data.      # Create variables to hold the FASTA label and data.
1063      my ($fastaLabel, $fastaData);      my ($fastaLabel, $fastaData);
1064      # Check for a feature specification.      Trace("FASTA desired type is $desiredType.") if T(4);
1065        # Check for a feature specification. The smoking gun for that is a vertical bar.
1066      if ($sequence =~ /^\s*(\w+\|\S+)\s*$/) {      if ($sequence =~ /^\s*(\w+\|\S+)\s*$/) {
1067          # Here we have a feature ID in $1. We'll need the Sprout object to process          # Here we have a feature ID in $1. We'll need the Sprout object to process
1068          # it.          # it.
1069          my $fid = $1;          my $fid = $1;
1070            Trace("Feature ID for fasta is $fid.") if T(3);
1071          my $sprout = $self->DB();          my $sprout = $self->DB();
1072          # Get the FIG ID. Note that we only use the first feature found. We are not          # Get the FIG ID. Note that we only use the first feature found. We are not
1073          # supposed to have redundant aliases, though we may have an ID that doesn't          # supposed to have redundant aliases, though we may have an ID that doesn't
1074          # exist.          # exist.
1075          my ($figID) = $sprout->FeaturesByAlias($fid);          my ($figID) = $sprout->FeaturesByAlias($fid);
1076          if (! $figID) {          if (! $figID) {
1077              $self->SetMessage("No feature found with the ID \"$fid\".");              $self->SetMessage("No gene found with the ID \"$fid\".");
1078                $okFlag = 0;
1079          } else {          } else {
1080              # Set the FASTA label.              # Set the FASTA label. The ID is the first favored alias.
1081              my $fastaLabel = $fid;              my $favored = $self->Q()->param('FavoredAlias') || 'fig';
1082                my $favorLen = length $favored;
1083                ($fastaLabel) = grep { substr($_, 0, $favorLen) eq $favored } $sprout->FeatureAliases($fid);
1084                if (! $fastaLabel) {
1085                    # In an emergency, fall back to the original ID.
1086                    $fastaLabel = $fid;
1087                }
1088              # Now proceed according to the sequence type.              # Now proceed according to the sequence type.
1089              if ($desiredType =~ /prot/i) {              if ($desiredType eq 'prot') {
1090                  # We want protein, so get the translation.                  # We want protein, so get the translation.
1091                  $fastaData = $sprout->FeatureTranslation($figID);                  $fastaData = $sprout->FeatureTranslation($figID);
1092                    Trace(length $fastaData . " characters returned for translation of $fastaLabel.") if T(3);
1093              } else {              } else {
1094                  # We want DNA, so get the DNA sequence. This is a two-step process.                  # We want DNA, so get the DNA sequence. This is a two-step process.
1095                  my @locList = $sprout->FeatureLocation($figID);                  my @locList = $sprout->FeatureLocation($figID);
1096                  $fastaData = $sprout->DNASeq(\@locList);                  $fastaData = $sprout->DNASeq(\@locList);
1097                    Trace(length $fastaData . " characters returned for DNA of $fastaLabel.") if T(3);
1098              }              }
1099          }          }
     } elsif ($incomingType =~ /prot/ && $desiredType =~ /dna/) {  
         # Here we're being asked to do an impossible conversion.  
         $self->SetMessage("Cannot convert a protein sequence to DNA.");  
1100      } else {      } else {
1101            Trace("Analyzing FASTA sequence.") if T(4);
1102          # Here we are expecting a FASTA. We need to see if there's a label.          # Here we are expecting a FASTA. We need to see if there's a label.
1103          if ($sequence =~ /^>\s*(\S.*)\s*\n(.+)$/) {          if ($sequence =~ /^>[\n\s]*(\S[^\n]*)\n(.+)$/s) {
1104                Trace("Label \"$1\" found in match to sequence:\n$sequence") if T(4);
1105              # Here we have a label, so we split it from the data.              # Here we have a label, so we split it from the data.
1106              $fastaLabel = $1;              $fastaLabel = $1;
1107              $fastaData = $2;              $fastaData = $2;
1108          } else {          } else {
1109                Trace("No label found in match to sequence:\n$sequence") if T(4);
1110              # Here we have no label, so we create one and use the entire sequence              # Here we have no label, so we create one and use the entire sequence
1111              # as data.              # as data.
1112              $fastaLabel = "User-specified $incomingType sequence";              $fastaLabel = "User-specified $desiredType sequence";
1113              $fastaData = $sequence;              $fastaData = $sequence;
1114          }          }
1115          # The next step is to clean the junk out of the sequence.          # The next step is to clean the junk out of the sequence.
1116          $fastaData =~ s/\n//g;          $fastaData =~ s/\n//g;
1117          $fastaData =~ s/\s+//g;          $fastaData =~ s/\s+//g;
1118          # Finally, if the user wants to convert to protein, we do it here. Note that          # Finally, verify that it's DNA if we're doing DNA stuff.
1119          # we've already prevented a conversion from protein to DNA.          if ($desiredType eq 'dna' && $fastaData =~ /[^agctxn]/i) {
1120          if ($incomingType ne $desiredType) {              $self->SetMessage("Invalid characters detected. Is the input really a DNA sequence?");
1121              $fastaData = Sprout::Protein($fastaData);              $okFlag = 0;
1122          }          }
1123      }      }
1124      # At this point, either "$fastaLabel" and "$fastaData" have values or an error is      Trace("FASTA data sequence: $fastaData") if T(4);
1125      # in progress.      # Only proceed if no error was detected.
1126      if (defined $fastaLabel) {      if ($okFlag) {
1127          # We need to format the sequence into 60-byte chunks. We use the infamous          # We need to format the sequence into 60-byte chunks. We use the infamous
1128          # grep-split trick. The split, because of the presence of the parentheses,          # grep-split trick. The split, because of the presence of the parentheses,
1129          # includes the matched delimiters in the output list. The grep strips out          # includes the matched delimiters in the output list. The grep strips out
1130          # the empty list items that appear between the so-called delimiters, since          # the empty list items that appear between the so-called delimiters, since
1131          # the delimiters are what we want.          # the delimiters are what we want.
1132          my @chunks = grep { $_ } split /(.{1,60})/, $fastaData;          my @chunks = grep { $_ } split /(.{1,60})/, $fastaData;
1133          my $retVal = join("\n", ">$fastaLabel", @chunks, "");          $retVal = join("\n", ">$fastaLabel", @chunks, "");
1134      }      }
1135      # Return the result.      # Return the result.
1136      return $retVal;      return $retVal;
1137  }  }
1138    
1139    =head3 SubsystemTree
1140    
1141    C<< my $tree = SearchHelper::SubsystemTree($sprout, %options); >>
1142    
1143    This method creates a subsystem selection tree suitable for passing to
1144    L</SelectionTree>. Each leaf node in the tree will have a link to the
1145    subsystem display page. In addition, each node can have a radio button. The
1146    radio button alue is either C<classification=>I<string>, where I<string> is
1147    a classification string, or C<id=>I<string>, where I<string> is a subsystem ID.
1148    Thus, it can either be used to filter by a group of related subsystems or a
1149    single subsystem.
1150    
1151    =over 4
1152    
1153    =item sprout
1154    
1155    Sprout database object used to get the list of subsystems.
1156    
1157    =item options
1158    
1159    Hash containing options for building the tree.
1160    
1161    =item RETURN
1162    
1163    Returns a reference to a tree list suitable for passing to L</SelectionTree>.
1164    
1165    =back
1166    
1167    The supported options are as follows.
1168    
1169    =over 4
1170    
1171    =item radio
1172    
1173    TRUE if the tree should be configured for radio buttons. The default is FALSE.
1174    
1175    =item links
1176    
1177    TRUE if the tree should be configured for links. The default is TRUE.
1178    
1179    =back
1180    
1181    =cut
1182    
1183    sub SubsystemTree {
1184        # Get the parameters.
1185        my ($sprout, %options) = @_;
1186        # Process the options.
1187        my $optionThing = Tracer::GetOptions({ radio => 0, links => 1 }, \%options);
1188        # Read in the subsystems.
1189        my @subs = $sprout->GetAll(['Subsystem'], "ORDER BY Subsystem(classification), Subsystem(id)", [],
1190                                   ['Subsystem(classification)', 'Subsystem(id)']);
1191        # Put any unclassified subsystems at the end. They will always be at the beginning, so if one
1192        # is at the end, ALL subsystems are unclassified and we don't bother.
1193        if ($#subs >= 0 && $subs[$#subs]->[0] ne '') {
1194            while ($subs[0]->[0] eq '') {
1195                my $classLess = shift @subs;
1196                push @subs, $classLess;
1197            }
1198        }
1199        # Declare the return variable.
1200        my @retVal = ();
1201        # Each element in @subs represents a leaf node, so as we loop through it we will be
1202        # producing one leaf node at a time. The leaf node is represented as a 2-tuple. The
1203        # first element is a semi-colon-delimited list of the classifications for the
1204        # subsystem. There will be a stack of currently-active classifications, which we will
1205        # compare to the incoming classifications from the end backward. A new classification
1206        # requires starting a new branch. A different classification requires closing an old
1207        # branch and starting a new one. Each classification in the stack will also contain
1208        # that classification's current branch. We'll add a fake classification at the
1209        # beginning that we can use to represent the tree as a whole.
1210        my $rootName = '<root>';
1211        # Create the classification stack. Note the stack is a pair of parallel lists,
1212        # one containing names and the other containing content.
1213        my @stackNames = ($rootName);
1214        my @stackContents = (\@retVal);
1215        # Add a null entry at the end of the subsystem list to force an unrolling.
1216        push @subs, ['', undef];
1217        # Loop through the subsystems.
1218        for my $sub (@subs) {
1219            # Pull out the classification list and the subsystem ID.
1220            my ($classString, $id) = @{$sub};
1221            Trace("Processing class \"$classString\" and subsystem $id.") if T(4);
1222            # Convert the classification string to a list with the root classification in
1223            # the front.
1224            my @classList = ($rootName, split($FIG_Config::splitter, $classString));
1225            # Find the leftmost point at which the class list differs from the stack.
1226            my $matchPoint = 0;
1227            while ($matchPoint <= $#stackNames && $matchPoint <= $#classList &&
1228                   $stackNames[$matchPoint] eq $classList[$matchPoint]) {
1229                $matchPoint++;
1230            }
1231            Trace("Match point is $matchPoint. Stack length is " . scalar(@stackNames) .
1232                  ". Class List length is " . scalar(@classList) . ".") if T(4);
1233            # Unroll the stack to the matchpoint.
1234            while ($#stackNames >= $matchPoint) {
1235                my $popped = pop @stackNames;
1236                pop @stackContents;
1237                Trace("\"$popped\" popped from stack.") if T(4);
1238            }
1239            # Start branches for any new classifications.
1240            while ($#stackNames < $#classList) {
1241                # The branch for a new classification contains its radio button
1242                # data and then a list of children. So, at this point, if radio buttons
1243                # are desired, we put them into the content.
1244                my $newLevel = scalar(@stackNames);
1245                my @newClassContent = ();
1246                if ($optionThing->{radio}) {
1247                    my $newClassString = join($FIG_Config::splitter, @classList[1..$newLevel]);
1248                    push @newClassContent, { value => "classification=$newClassString%" };
1249                }
1250                # The new classification node is appended to its parent's content
1251                # and then pushed onto the stack. First, we need the node name.
1252                my $nodeName = $classList[$newLevel];
1253                # Add the classification to its parent. This makes it part of the
1254                # tree we'll be returning to the user.
1255                push @{$stackContents[$#stackNames]}, $nodeName, \@newClassContent;
1256                # Push the classification onto the stack.
1257                push @stackContents, \@newClassContent;
1258                push @stackNames, $nodeName;
1259                Trace("\"$nodeName\" pushed onto stack.") if T(4);
1260            }
1261            # Now the stack contains all our parent branches. We add the subsystem to
1262            # the branch at the top of the stack, but only if it's NOT the dummy node.
1263            if (defined $id) {
1264                # Compute the node name from the ID.
1265                my $nodeName = $id;
1266                $nodeName =~ s/_/ /g;
1267                # Create the node's leaf hash. This depends on the value of the radio
1268                # and link options.
1269                my $nodeContent = {};
1270                if ($optionThing->{links}) {
1271                    # Compute the link value.
1272                    my $linkable = uri_escape($id);
1273                    $nodeContent->{link} = "../FIG/display_subsys.cgi?ssa_name=$linkable;request=show_ssa;sort=by_phylo;show_clusters=1;SPROUT=1";
1274                }
1275                if ($optionThing->{radio}) {
1276                    # Compute the radio value.
1277                    $nodeContent->{value} = "id=$id";
1278                }
1279                # Push the node into its parent branch.
1280                Trace("\"$nodeName\" added to node list.") if T(4);
1281                push @{$stackContents[$#stackNames]}, $nodeName, $nodeContent;
1282            }
1283        }
1284        # Return the result.
1285        return \@retVal;
1286    }
1287    
1288    
1289  =head3 NmpdrGenomeMenu  =head3 NmpdrGenomeMenu
1290    
1291  C<< my $htmlText = $shelp->NmpdrGenomeMenu($menuName, $multiple, \@selected, $rows); >>  C<< my $htmlText = $shelp->NmpdrGenomeMenu($menuName, $multiple, \@selected, $rows); >>
# Line 1082  Line 1315 
1315  Number of rows to display. If omitted, the default is 1 for a single-select list  Number of rows to display. If omitted, the default is 1 for a single-select list
1316  and 10 for a multi-select list.  and 10 for a multi-select list.
1317    
1318    =item crossMenu (optional)
1319    
1320    If specified, is presumed to be the name of another genome menu whose contents
1321    are to be mutually exclusive with the contents of this menu. As a result, instead
1322    of the standard onChange event, the onChange event will deselect any entries in
1323    the other menu.
1324    
1325  =item RETURN  =item RETURN
1326    
1327  Returns the HTML text to generate a C<SELECT> menu inside a form.  Returns the HTML text to generate a C<SELECT> menu inside a form.
# Line 1092  Line 1332 
1332    
1333  sub NmpdrGenomeMenu {  sub NmpdrGenomeMenu {
1334      # Get the parameters.      # Get the parameters.
1335      my ($self, $menuName, $multiple, $selected, $rows) = @_;      my ($self, $menuName, $multiple, $selected, $rows, $cross) = @_;
1336      # Get the Sprout and CGI objects.      # Get the Sprout and CGI objects.
1337      my $sprout = $self->DB();      my $sprout = $self->DB();
1338      my $cgi = $self->Q();      my $cgi = $self->Q();
# Line 1126  Line 1366 
1366          for my $genome (@genomeList) {          for my $genome (@genomeList) {
1367              # Get the genome data.              # Get the genome data.
1368              my ($group, $genomeID, $genus, $species, $strain) = @{$genome};              my ($group, $genomeID, $genus, $species, $strain) = @{$genome};
1369              # Form the genome name.              # Compute and cache its name and display group.
1370              my $name = "$genus $species";              my ($name, $displayGroup) = $self->SaveOrganismData($group, $genomeID, $genus, $species,
1371              if ($strain) {                                                                  $strain);
1372                  $name .= " $strain";              # Push the genome into the group's list. Note that we use the real group
1373              }              # name here, not the display group name.
             # Push the genome into the group's list.  
1374              push @{$gHash{$group}}, [$genomeID, $name];              push @{$gHash{$group}}, [$genomeID, $name];
1375          }          }
1376          # Save the genome list for future use.          # Save the genome list for future use.
# Line 1148  Line 1387 
1387      if (defined $selected) {      if (defined $selected) {
1388          %selectedHash = map { $_ => 1 } grep { defined($_) } @{$selected};          %selectedHash = map { $_ => 1 } grep { defined($_) } @{$selected};
1389      }      }
1390      # Now it gets complicated. We need a way to mark all the NMPDR genomes.      # Now it gets complicated. We need a way to mark all the NMPDR genomes. We take advantage
1391        # of the fact they come first in the list. We'll accumulate a count of the NMPDR genomes
1392        # and use that to make the selections.
1393        my $nmpdrCount = 0;
1394      # Create the type counters.      # Create the type counters.
1395      my $groupCount = 1;      my $groupCount = 1;
1396      # Compute the ID for the status display.      # Compute the ID for the status display.
# Line 1157  Line 1399 
1399      my $showSelect = "showSelected($menuName, '$divID', 1000);";      my $showSelect = "showSelected($menuName, '$divID', 1000);";
1400      # If multiple selection is supported, create an onChange event.      # If multiple selection is supported, create an onChange event.
1401      my $onChange = "";      my $onChange = "";
1402      if ($multiple) {      if ($cross) {
1403            # Here we have a paired menu. Selecting something in our menu unselects it in the
1404            # other and redisplays the status of both.
1405            $onChange = " onChange=\"crossUnSelect($menuName, '$divID', $cross, '${formName}_${cross}_status', 1000)\"";
1406        } elsif ($multiple) {
1407            # This is an unpaired menu, so all we do is redisplay our status.
1408          $onChange = " onChange=\"$showSelect\"";          $onChange = " onChange=\"$showSelect\"";
1409      }      }
1410      # Create the SELECT tag and stuff it into the output array.      # Create the SELECT tag and stuff it into the output array.
1411      my $select = "<SELECT name=\"$menuName\"$onChange$multipleTag size=\"$rows\">";      my @lines = ("<SELECT name=\"$menuName\"$onChange$multipleTag size=\"$rows\">");
     my @lines = ($select);  
1412      # Loop through the groups.      # Loop through the groups.
1413      for my $group (@groups) {      for my $group (@groups) {
1414          # Create the option group tag.          # Create the option group tag.
1415          my $tag = "<OPTGROUP label=\"$group\">";          my $tag = "<OPTGROUP label=\"$group\">";
1416          push @lines, "  $tag";          push @lines, "  $tag";
         # Compute the label for this group's options. This is seriously dirty stuff, as the  
         # label option may have functionality in future browsers. If that happens, we'll need  
         # to modify the genome text so that the "selectSome" method can tell which are NMPDR  
         # organisms and which aren't. Sadly, the OPTGROUP tag is invisible in the DOM Javascript  
         # hierarchy, so we can't use it.  
         my $label = ($group eq $FIG_Config::otherGroup ? "other" : "nmpdr");  
1417          # Get the genomes in the group.          # Get the genomes in the group.
1418          for my $genome (@{$groupHash->{$group}}) {          for my $genome (@{$groupHash->{$group}}) {
1419                # Count this organism if it's NMPDR.
1420                if ($group ne $FIG_Config::otherGroup) {
1421                    $nmpdrCount++;
1422                }
1423                # Get the organism ID and name.
1424              my ($genomeID, $name) = @{$genome};              my ($genomeID, $name) = @{$genome};
1425              # See if it's selected.              # See if it's selected.
1426              my $select = ($selectedHash{$genomeID} ? " selected" : "");              my $select = ($selectedHash{$genomeID} ? " selected" : "");
1427              # Generate the option tag.              # Generate the option tag.
1428              my $optionTag = "<OPTION value=\"$genomeID\" label=\"$label\"$select>$name <em>($genomeID)</em></OPTION>";              my $optionTag = "<OPTION value=\"$genomeID\"$select>$name <em>($genomeID)</em></OPTION>";
1429              push @lines, "    $optionTag";              push @lines, "    $optionTag";
1430          }          }
1431          # Close the option group.          # Close the option group.
# Line 1190  Line 1435 
1435      push @lines, "</SELECT>";      push @lines, "</SELECT>";
1436      # Check for multiple selection.      # Check for multiple selection.
1437      if ($multiple) {      if ($multiple) {
1438          # Since multi-select is on, we set up some buttons to set and clear selections.          # Multi-select is on, so we need to add some selection helpers. First is
1439          push @lines, "<br />";          # the search box. This allows the user to type text and have all genomes containing
         push @lines, "<INPUT type=\"button\" name=\"SelectAll\" class=\"bigButton\" value=\"Select All\" onClick=\"selectAll($menuName); $showSelect\" />";  
         push @lines, "<INPUT type=\"button\" name=\"ClearAll\" class=\"bigButton\"  value=\"Clear All\" onClick=\"clearAll($menuName); $showSelect\" />";  
         push @lines, "<INPUT type=\"button\" name=\"NMPDROnly\" class=\"bigButton\"  value=\"Select NMPDR\" onClick=\"selectSome($menuName, 'nmpdr'); $showSelect\" />";  
         push @lines, "<INPUT type=\"button\" name=\"OtherOnly\" class=\"bigButton\" value=\"Select Supporting\" onClick=\"selectSome($menuName, 'other'); $showSelect\" />";  
         # Now add the search box. This allows the user to type text and have all genomes containing  
1440          # the text selected automatically.          # the text selected automatically.
1441          my $searchThingName = "${menuName}_SearchThing";          my $searchThingName = "${menuName}_SearchThing";
1442          push @lines, "<br>Select genomes containing <INPUT type=\"text\" name=\"$searchThingName\" size=\"30\" />&nbsp;" .          push @lines, "<br />" .
1443                       "<INPUT type=\"button\" name=\"Select\" class=\"button\" value=\"Search\" onClick=\"selectViaSearch($menuName, $searchThingName); $showSelect\" />";                       "<INPUT type=\"button\" name=\"Search\" class=\"button\" value=\"Select genomes containing\" onClick=\"selectViaSearch($menuName, $searchThingName); $showSelect\" />&nbsp;" .
1444                         "<INPUT type=\"text\" name=\"$searchThingName\" size=\"30\" />";
1445            # Next are the buttons to set and clear selections.
1446            push @lines, "<br />";
1447            push @lines, "<INPUT type=\"button\" name=\"ClearAll\" class=\"bigButton\"  value=\"Clear All\" onClick=\"clearAll($menuName); $showSelect\" />";
1448            push @lines, "<INPUT type=\"button\" name=\"SelectAll\" class=\"bigButton\" value=\"Select All\" onClick=\"selectAll($menuName); $showSelect\" />";
1449            push @lines, "<INPUT type=\"button\" name=\"NMPDROnly\" class=\"bigButton\"  value=\"Select NMPDR\" onClick=\"selectSome($menuName, $nmpdrCount, true); $showSelect\" />";
1450            push @lines, "<INPUT type=\"button\" name=\"OtherOnly\" class=\"bigButton\" value=\"Select Supporting\" onClick=\"selectSome($menuName, $nmpdrCount, false); $showSelect\" />";
1451          # Add the status display, too.          # Add the status display, too.
1452          push @lines, "<DIV id=\"$divID\" class=\"selectStatus\"></DIV>";          push @lines, "<DIV id=\"$divID\" class=\"selectStatus\"></DIV>";
1453          # Queue to update the status display when the form loads. We need to modify the show statement          # Queue to update the status display when the form loads. We need to modify the show statement
# Line 1287  Line 1534 
1534  =item rows  =item rows
1535    
1536  Reference to a list of table rows. Each table row must be in HTML form with all  Reference to a list of table rows. Each table row must be in HTML form with all
1537  the TR and TD tags set up. The first TD or TH tag in each row will be modified to  the TR and TD tags set up. The first TD or TH tag in the first non-colspanned row
1538  set the width. Everything else will be left as is.  will be modified to set the width. Everything else will be left as is.
1539    
1540  =item RETURN  =item RETURN
1541    
# Line 1303  Line 1550 
1550      my ($self, $rows) = @_;      my ($self, $rows) = @_;
1551      # Get the CGI object.      # Get the CGI object.
1552      my $cgi = $self->Q();      my $cgi = $self->Q();
1553      # Fix the widths on the first column. Note that we eschew the use of the "g"      # The first column of the first row must have its width fixed.
1554        # This flag will be set to FALSE when that happens.
1555        my $needWidth = 1;
1556      # modifier becase we only want to change the first tag. Also, if a width      # modifier becase we only want to change the first tag. Also, if a width
1557      # is already specified on the first column bad things will happen.      # is already specified on the first column bad things will happen.
1558      for my $row (@{$rows}) {      for my $row (@{$rows}) {
1559          $row =~ s/(<td|th)/$1 width="150"/i;          # See if this row needs a width.
1560            if ($needWidth && $row =~ /<(td|th) ([^>]+)>/i) {
1561                # Here we have a first cell and its tag parameters are in $2.
1562                my $elements = $2;
1563                if ($elements !~ /colspan/i) {
1564                    Trace("No colspan tag found in element \'$elements\'.") if T(3);
1565                    # Here there's no colspan, so we plug in the width. We
1566                    # eschew the "g" modifier on the substitution because we
1567                    # only want to update the first cell.
1568                    $row =~ s/(<(td|th))/$1 width="150"/i;
1569                    # Denote we don't need this any more.
1570                    $needWidth = 0;
1571                }
1572            }
1573      }      }
1574      # Create the table.      # Create the table.
1575      my $retVal = $cgi->table({border => 2, cellspacing => 2,      my $retVal = $cgi->table({border => 2, cellspacing => 2,
# Line 1319  Line 1581 
1581    
1582  =head3 SubmitRow  =head3 SubmitRow
1583    
1584  C<< my $htmlText = $shelp->SubmitRow(); >>  C<< my $htmlText = $shelp->SubmitRow($caption); >>
1585    
1586  Returns the HTML text for the row containing the page size control  Returns the HTML text for the row containing the page size control
1587  and the submit button. All searches should have this row somewhere  and the submit button. All searches should have this row somewhere
1588  near the top of the form.  near the top of the form.
1589    
1590    =over 4
1591    
1592    =item caption (optional)
1593    
1594    Caption to be put on the search button. The default is C<Go>.
1595    
1596    =item RETURN
1597    
1598    Returns a table row containing the controls for submitting the search
1599    and tuning the results.
1600    
1601    =back
1602    
1603  =cut  =cut
1604    
1605  sub SubmitRow {  sub SubmitRow {
1606      # Get the parameters.      # Get the parameters.
1607      my ($self) = @_;      my ($self, $caption) = @_;
1608      my $cgi = $self->Q();      my $cgi = $self->Q();
1609        # Compute the button caption.
1610        my $realCaption = (defined $caption ? $caption : 'Go');
1611      # Get the current page size.      # Get the current page size.
1612      my $pageSize = $cgi->param('PageSize');      my $pageSize = $cgi->param('PageSize');
1613      # Get the incoming external-link flag.      # Get the incoming external-link flag.
# Line 1338  Line 1615 
1615      # Create the row.      # Create the row.
1616      my $retVal = $cgi->Tr($cgi->td("Results/Page"),      my $retVal = $cgi->Tr($cgi->td("Results/Page"),
1617                            $cgi->td($cgi->popup_menu(-name => 'PageSize',                            $cgi->td($cgi->popup_menu(-name => 'PageSize',
1618                                                      -values => [10, 25, 45, 100, 1000],                                                      -values => [10, 25, 50, 100, 1000],
1619                                                      -default => $pageSize) . " " .                                                      -default => $pageSize)),
                                    $cgi->checkbox(-name => 'ShowURL',  
                                                   -value => 1,  
                                                   -label => 'Show URL')),  
1620                            $cgi->td($cgi->submit(-class => 'goButton',                            $cgi->td($cgi->submit(-class => 'goButton',
1621                                                  -name => 'Search',                                                  -name => 'Search',
1622                                                  -value => 'Go')));                                                  -value => $realCaption)));
1623      # Return the result.      # Return the result.
1624      return $retVal;      return $retVal;
1625  }  }
1626    
1627  =head3 FeatureFilterRows  =head3 FeatureFilterRows
1628    
1629  C<< my $htmlText = $shelp->FeatureFilterRows(); >>  C<< my $htmlText = $shelp->FeatureFilterRows(@subset); >>
1630    
1631    This method creates table rows that can be used to filter features. The form
1632    values can be used to select features by genome using the B<FeatureQuery>
1633    object.
1634    
1635    =over 4
1636    
1637    =item subset
1638    
1639  This method creates table rows that can be used to filter features. There are  List of rows to display. The default (C<all>) is to display all rows.
1640  two rows returned, and the values can be used to select features by genome  C<words> displays the word search box, C<subsys> displays the subsystem
1641  using the B<FeatureQuery> object.  selector, and C<options> displays the options row.
1642    
1643    =item RETURN
1644    
1645    Returns the html text for table rows containing the desired feature filtering controls.
1646    
1647    =back
1648    
1649  =cut  =cut
1650    
1651  sub FeatureFilterRows {  sub FeatureFilterRows {
1652      # Get the parameters.      # Get the parameters.
1653      my ($self) = @_;      my ($self, @subset) = @_;
1654        if (@subset == 0 || $subset[0] eq 'all') {
1655            @subset = qw(words subsys options);
1656        }
1657      # Return the result.      # Return the result.
1658      return FeatureQuery::FilterRows($self);      return FeatureQuery::FilterRows($self, @subset);
1659  }  }
1660    
1661  =head3 GBrowseFeatureURL  =head3 GBrowseFeatureURL
# Line 1406  Line 1697 
1697          # Get the feature location string.          # Get the feature location string.
1698          my $loc = $sprout->FeatureLocation($feat);          my $loc = $sprout->FeatureLocation($feat);
1699          # Compute the contig, start, and stop points.          # Compute the contig, start, and stop points.
1700          my($start, $stop, $contig) = BasicLocation::Parse($loc);          my($contig, $start, $stop) = BasicLocation::Parse($loc);
1701            Trace("Start and stop are ($start,$stop) on contig $contig.") if T(3);
1702          # Now we need to do some goofiness to insure that the location is not too          # Now we need to do some goofiness to insure that the location is not too
1703          # big and that we get some surrounding stuff.          # big and that we get some surrounding stuff.
1704          my $mid = int(($start + $stop) / 2);          my $mid = int(($start + $stop) / 2);
# Line 1436  Line 1728 
1728          }          }
1729          my $seg_id = $contig;          my $seg_id = $contig;
1730          $seg_id =~ s/:/--/g;          $seg_id =~ s/:/--/g;
1731            Trace("Show limits are ($show_start,$show_stop) in genome $genomeID with ref $seg_id.") if T(3);
1732          # Assemble all the pieces.          # Assemble all the pieces.
1733          $retVal = "gbrowse.cgi/GB_$genomeID?ref=$seg_id&start=$show_start&stop=$show_stop";          $retVal = "gbrowse.cgi/GB_$genomeID?ref=$seg_id;start=$show_start;stop=$show_stop";
1734      }      }
1735      # Return the result.      # Return the result.
1736      return $retVal;      return $retVal;
# Line 1530  Line 1823 
1823    
1824  =head3 ComputeSearchURL  =head3 ComputeSearchURL
1825    
1826  C<< my $url = $shelp->ComputeSearchURL(); >>  C<< my $url = $shelp->ComputeSearchURL(%overrides); >>
1827    
1828  Compute the GET-style URL for the current search. In order for this to work, there  Compute the GET-style URL for the current search. In order for this to work, there
1829  must be a copy of the search form on the current page. This will always be the  must be a copy of the search form on the current page. This will always be the
# Line 1540  Line 1833 
1833  main complication is that if the user specified all genomes, we'll want to  main complication is that if the user specified all genomes, we'll want to
1834  remove the parameter entirely from a get-style URL.  remove the parameter entirely from a get-style URL.
1835    
1836    =over 4
1837    
1838    =item overrides
1839    
1840    Hash containing override values for the parameters, where the parameter name is
1841    the key and the parameter value is the override value. If the override value is
1842    C<undef>, the parameter will be deleted from the result.
1843    
1844    =item RETURN
1845    
1846    Returns a GET-style URL for invoking the search with the specified overrides.
1847    
1848    =back
1849    
1850  =cut  =cut
1851    
1852  sub ComputeSearchURL {  sub ComputeSearchURL {
1853      # Get the parameters.      # Get the parameters.
1854      my ($self) = @_;      my ($self, %overrides) = @_;
1855      # Get the database and CGI query object.      # Get the database and CGI query object.
1856      my $cgi = $self->Q();      my $cgi = $self->Q();
1857      my $sprout = $self->DB();      my $sprout = $self->DB();
# Line 1571  Line 1878 
1878          # a singleton list, but that's okay.          # a singleton list, but that's okay.
1879          my @values = split (/\0/, $parms{$parmKey});          my @values = split (/\0/, $parms{$parmKey});
1880          # Check for special cases.          # Check for special cases.
1881          if ($parmKey eq 'featureTypes') {          if (grep { $_ eq $parmKey } qw(SessionID ResultCount Page PageSize Trace TF)) {
             # Here we need to see if the user wants all the feature types. If he  
             # does, we erase all the values so that the parameter is not output.  
             my %valueCheck = map { $_ => 1 } @values;  
             my @list = FeatureQuery::AllFeatureTypes();  
             my $okFlag = 1;  
             for (my $i = 0; $okFlag && $i <= $#list; $i++) {  
                 if (! $valueCheck{$list[$i]}) {  
                     $okFlag = 0;  
                 }  
             }  
             if ($okFlag) {  
                 @values = ();  
             }  
         } elsif (grep { $_ eq $parmKey } qw(SessionID ResultCount Page PageSize Trace TF ShowURL)) {  
1882              # These are bookkeeping parameters we don't need to start a search.              # These are bookkeeping parameters we don't need to start a search.
1883              @values = ();              @values = ();
1884          } elsif ($parmKey =~ /_SearchThing$/) {          } elsif ($parmKey =~ /_SearchThing$/) {
# Line 1599  Line 1892 
1892              if ($allFlag) {              if ($allFlag) {
1893                  @values = ();                  @values = ();
1894              }              }
1895            } elsif (exists $overrides{$parmKey}) {
1896                # Here the value is being overridden, so we skip it for now.
1897                @values = ();
1898          }          }
1899          # If we still have values, create the URL parameters.          # If we still have values, create the URL parameters.
1900          if (@values) {          if (@values) {
1901              push @urlList, map { "$parmKey=" . uri_escape($_) } @values;              push @urlList, map { "$parmKey=" . uri_escape($_) } @values;
1902          }          }
1903      }      }
1904        # Now do the overrides.
1905        for my $overKey (keys %overrides) {
1906            # Only use this override if it's not a delete marker.
1907            if (defined $overrides{$overKey}) {
1908                push @urlList, "$overKey=" . uri_escape($overrides{$overKey});
1909            }
1910        }
1911      # Add the parameters to the URL.      # Add the parameters to the URL.
1912      $retVal .= "?" . join(";", @urlList);      $retVal .= "?" . join(";", @urlList);
1913      # Return the result.      # Return the result.
# Line 1647  Line 1950 
1950      return $retVal;      return $retVal;
1951  }  }
1952    
1953    =head3 AdvancedClassList
1954    
1955    C<< my @classes = SearchHelper::AdvancedClassList(); >>
1956    
1957    Return a list of advanced class names. This list is used to generate the directory
1958    of available searches on the search page.
1959    
1960    We use the %INC variable to accomplish this.
1961    
1962    =cut
1963    
1964    sub AdvancedClassList {
1965        my @retVal = map { $_ =~ /^SH(\w+)\.pm/; $1 } grep { $_ =~ /^SH/ } keys %INC;
1966        return sort @retVal;
1967    }
1968    
1969    =head3 SelectionTree
1970    
1971    C<< my $htmlText = SearchHelper::SelectionTree($cgi, \%tree, %options); >>
1972    
1973    Display a selection tree.
1974    
1975    This method creates the HTML for a tree selection control. The tree is implemented as a set of
1976    nested HTML unordered lists. Each selectable element of the tree will contain a radio button. In
1977    addition, some of the tree nodes can contain hyperlinks.
1978    
1979    The tree itself is passed in as a multi-level list containing node names followed by
1980    contents. Each content element is a reference to a similar list. The first element of
1981    each list may be a hash reference. If so, it should contain one or both of the following
1982    keys.
1983    
1984    =over 4
1985    
1986    =item link
1987    
1988    The navigation URL to be popped up if the user clicks on the node name.
1989    
1990    =item value
1991    
1992    The form value to be returned if the user selects the tree node.
1993    
1994    =back
1995    
1996    The presence of a C<link> key indicates the node name will be hyperlinked. The presence of
1997    a C<value> key indicates the node name will have a radio button. If a node has no children,
1998    you may pass it a hash reference instead of a list reference.
1999    
2000    The following example shows the hash for a three-level tree with links on the second level and
2001    radio buttons on the third.
2002    
2003        [   Objects => [
2004                Entities => [
2005                    {link => "../docs/WhatIsAnEntity.html"},
2006                    Genome => {value => 'GenomeData'},
2007                    Feature => {value => 'FeatureData'},
2008                    Contig => {value => 'ContigData'},
2009                ],
2010                Relationships => [
2011                    {link => "../docs/WhatIsARelationShip.html"},
2012                    HasFeature => {value => 'GenomeToFeature'},
2013                    IsOnContig => {value => 'FeatureToContig'},
2014                ]
2015            ]
2016        ]
2017    
2018    Note how each leaf of the tree has a hash reference for its value, while the branch nodes
2019    all have list references.
2020    
2021    This next example shows how to set up a taxonomy selection field. The value returned
2022    by the tree control will be the taxonomy string for the selected node ready for use
2023    in a LIKE-style SQL filter. Only the single branch ending in campylobacter is shown for
2024    reasons of space.
2025    
2026        [   All => [
2027                {value => "%"},
2028                Bacteria => [
2029                    {value => "Bacteria%"},
2030                    Proteobacteria => [
2031                        {value => "Bacteria; Proteobacteria%"},
2032                        Epsilonproteobacteria => [
2033                            {value => "Bacteria; Proteobacteria;Epsilonproteobacteria%"},
2034                            Campylobacterales => [
2035                                {value => "Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales%"},
2036                                Campylobacteraceae =>
2037                                    {value => "Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales; Campylobacteraceae%"},
2038                                ...
2039                            ]
2040                            ...
2041                        ]
2042                        ...
2043                    ]
2044                    ...
2045                ]
2046                ...
2047            ]
2048        ]
2049    
2050    
2051    This method of tree storage allows the caller to control the order in which the tree nodes
2052    are displayed and to completely control value selection and use of hyperlinks. It is, however
2053    a bit complicated. Eventually, tree-building classes will be provided to simplify things.
2054    
2055    The parameters to this method are as follows.
2056    
2057    =over 4
2058    
2059    =item cgi
2060    
2061    CGI object used to generate the HTML.
2062    
2063    =item tree
2064    
2065    Reference to a hash describing a tree. See the description above.
2066    
2067    =item options
2068    
2069    Hash containing options for the tree display.
2070    
2071    =back
2072    
2073    The allowable options are as follows
2074    
2075    =over 4
2076    
2077    =item nodeImageClosed
2078    
2079    URL of the image to display next to the tree nodes when they are collapsed. Clicking
2080    on the image will expand a section of the tree. The default is C<../FIG/Html/plus.gif>.
2081    
2082    =item nodeImageOpen
2083    
2084    URL of the image to display next to the tree nodes when they are expanded. Clicking
2085    on the image will collapse a section of the tree. The default is C<../FIG/Html/minus.gif>.
2086    
2087    =item style
2088    
2089    Style to use for the tree. The default is C<tree>. Because the tree style is implemented
2090    as nested lists, the key components of this style are the definitions for the C<ul> and
2091    C<li> tags. The default style file contains the following definitions.
2092    
2093        .tree ul {
2094           margin-left: 0; padding-left: 22px
2095        }
2096        .tree li {
2097            list-style-type: none;
2098        }
2099    
2100    The default image is 22 pixels wide, so in the above scheme each tree level is indented from its
2101    parent by the width of the node image. This use of styles limits the things we can do in formatting
2102    the tree, but it has the advantage of vastly simplifying the tree creation.
2103    
2104    =item name
2105    
2106    Field name to give to the radio buttons in the tree. The default is C<selection>.
2107    
2108    =item target
2109    
2110    Frame target for links. The default is C<_self>.
2111    
2112    =item selected
2113    
2114    If specified, the value of the radio button to be pre-selected.
2115    
2116    =back
2117    
2118    =cut
2119    
2120    sub SelectionTree {
2121        # Get the parameters.
2122        my ($cgi, $tree, %options) = @_;
2123        # Get the options.
2124        my $optionThing = Tracer::GetOptions({ name => 'selection',
2125                                               nodeImageClosed => '../FIG/Html/plus.gif',
2126                                               nodeImageOpen => '../FIG/Html/minus.gif',
2127                                               style => 'tree',
2128                                               target => '_self',
2129                                               selected => undef},
2130                                             \%options);
2131        # Declare the return variable. We'll do the standard thing with creating a list
2132        # of HTML lines and rolling them together at the end.
2133        my @retVal = ();
2134        # Only proceed if the tree is present.
2135        if (defined($tree)) {
2136            # Validate the tree.
2137            if (ref $tree ne 'ARRAY') {
2138                Confess("Selection tree is not a list reference.");
2139            } elsif (scalar @{$tree} == 0) {
2140                # The tree is empty, so we do nothing.
2141            } elsif ($tree->[0] eq 'HASH') {
2142                Confess("Hash reference found at start of selection tree. The tree as a whole cannot have attributes, only tree nodes.");
2143            } else {
2144                # Here we have a real tree. Apply the tree style.
2145                push @retVal, $cgi->start_div({ class => $optionThing->{style} });
2146                # Give us a DIV ID.
2147                my $divID = GetDivID($optionThing->{name});
2148                # Show the tree.
2149                push @retVal, ShowBranch($cgi, "(root)", $divID, $tree, $optionThing, 'block');
2150                # Close the DIV block.
2151                push @retVal, $cgi->end_div();
2152            }
2153        }
2154        # Return the result.
2155        return join("\n", @retVal, "");
2156    }
2157    
2158    =head3 ShowBranch
2159    
2160    C<< my @htmlLines = SearchHelper::ShowBranch($cgi, $label, $id, $branch, $options, $displayType); >>
2161    
2162    This is a recursive method that displays a branch of the tree.
2163    
2164    =over 4
2165    
2166    =item cgi
2167    
2168    CGI object used to format HTML.
2169    
2170    =item label
2171    
2172    Label of this tree branch. It is only used in error messages.
2173    
2174    =item id
2175    
2176    ID to be given to this tree branch. The ID is used in the code that expands and collapses
2177    tree nodes.
2178    
2179    =item branch
2180    
2181    Reference to a list containing the content of the tree branch. The list contains an optional
2182    hash reference that is ignored and the list of children, each child represented by a name
2183    and then its contents. The contents could by a hash reference (indicating the attributes
2184    of a leaf node), or another tree branch.
2185    
2186    =item options
2187    
2188    Options from the original call to L</SelectionTree>.
2189    
2190    =item displayType
2191    
2192    C<block> if the contents of this list are to be displayed, C<none> if they are to be
2193    hidden.
2194    
2195    =item RETURN
2196    
2197    Returns one or more HTML lines that can be used to display the tree branch.
2198    
2199    =back
2200    
2201    =cut
2202    
2203    sub ShowBranch {
2204        # Get the parameters.
2205        my ($cgi, $label, $id, $branch, $options, $displayType) = @_;
2206        # Declare the return variable.
2207        my @retVal = ();
2208        # Start the branch.
2209        push @retVal, $cgi->start_ul({ id => $id, style => "display:$displayType" });
2210        # Check for the hash and choose the start location accordingly.
2211        my $i0 = (ref $branch->[0] eq 'HASH' ? 1 : 0);
2212        # Get the list length.
2213        my $i1 = scalar(@{$branch});
2214        # Verify we have an even number of elements.
2215        if (($i1 - $i0) % 2 != 0) {
2216            Trace("Branch elements are from $i0 to $i1.") if T(3);
2217            Confess("Odd number of elements in tree branch $label.");
2218        } else {
2219            # Loop through the elements.
2220            for (my $i = $i0; $i < $i1; $i += 2) {
2221                # Get this node's label and contents.
2222                my ($myLabel, $myContent) = ($branch->[$i], $branch->[$i+1]);
2223                # Get an ID for this node's children (if any).
2224                my $myID = GetDivID($options->{name});
2225                # Now we need to find the list of children and the options hash.
2226                # This is a bit ugly because we allow the shortcut of a hash without an
2227                # enclosing list. First, we need some variables.
2228                my $attrHash = {};
2229                my @childHtml = ();
2230                my $hasChildren = 0;
2231                if (! ref $myContent) {
2232                    Confess("Invalid tree definition. Scalar found as content of node \"$myLabel\".");
2233                } elsif (ref $myContent eq 'HASH') {
2234                    # Here the node is a leaf and its content contains the link/value hash.
2235                    $attrHash = $myContent;
2236                } elsif (ref $myContent eq 'ARRAY') {
2237                    # Here the node may be a branch. Its content is a list.
2238                    my $len = scalar @{$myContent};
2239                    if ($len >= 1) {
2240                        # Here the first element of the list could by the link/value hash.
2241                        if (ref $myContent->[0] eq 'HASH') {
2242                            $attrHash = $myContent->[0];
2243                            # If there's data in the list besides the hash, it's our child list.
2244                            # We can pass the entire thing as the child list, because the hash
2245                            # is ignored.
2246                            if ($len > 1) {
2247                                $hasChildren = 1;
2248                            }
2249                        } else {
2250                            $hasChildren = 1;
2251                        }
2252                        # If we have children, create the child list with a recursive call.
2253                        if ($hasChildren) {
2254                            Trace("Processing children of $myLabel.") if T(4);
2255                            push @childHtml, ShowBranch($cgi, $myLabel, $myID, $myContent, $options, 'none');
2256                            Trace("Children of $myLabel finished.") if T(4);
2257                        }
2258                    }
2259                }
2260                # Okay, it's time to pause and take stock. We have the label of the current node
2261                # in $myLabel, its attributes in $attrHash, and if it is NOT a leaf node, we
2262                # have a child list in @childHtml. If it IS a leaf node, $hasChildren is 0.
2263                # Compute the image HTML. It's tricky, because we have to deal with the open and
2264                # closed images.
2265                my @images = ($options->{nodeImageOpen}, $options->{nodeImageClosed});
2266                my $image = $images[$hasChildren];
2267                my $prefixHtml = $cgi->img({src => $image, id => "${myID}img"});
2268                if ($hasChildren) {
2269                    # If there are children, we wrap the image in a toggle hyperlink.
2270                    $prefixHtml = $cgi->a({ onClick => "javascript:treeToggle('$myID','$images[0]', '$images[1]')" },
2271                                          $prefixHtml);
2272                }
2273                # Now the radio button, if any. Note we use "defined" in case the user wants the
2274                # value to be 0.
2275                if (defined $attrHash->{value}) {
2276                    # Due to a glitchiness in the CGI stuff, we have to build the attribute
2277                    # hash for the "input" method. If the item is pre-selected, we add
2278                    # "checked => undef" to the hash. Otherwise, we can't have "checked"
2279                    # at all.
2280                    my $radioParms = { type => 'radio',
2281                                       name => $options->{name},
2282                                       value => $attrHash->{value},
2283                                     };
2284                    if (defined $options->{selected} && $options->{selected} eq $attrHash->{value}) {
2285                        $radioParms->{checked} = undef;
2286                    }
2287                    $prefixHtml .= $cgi->input($radioParms);
2288                }
2289                # Next, we format the label.
2290                my $labelHtml = $myLabel;
2291                Trace("Formatting tree node for \"$myLabel\".") if T(4);
2292                # Apply a hyperlink if necessary.
2293                if (defined $attrHash->{link}) {
2294                    $labelHtml = $cgi->a({ href => $attrHash->{link}, target => $options->{target} },
2295                                         $labelHtml);
2296                }
2297                # Finally, roll up the child HTML. If there are no children, we'll get a null string
2298                # here.
2299                my $childHtml = join("\n", @childHtml);
2300                # Now we have all the pieces, so we can put them together.
2301                push @retVal, $cgi->li("$prefixHtml$labelHtml$childHtml");
2302            }
2303        }
2304        # Close the tree branch.
2305        push @retVal, $cgi->end_ul();
2306        # Return the result.
2307        return @retVal;
2308    }
2309    
2310    =head3 GetDivID
2311    
2312    C<< my $idString = SearchHelper::GetDivID($name); >>
2313    
2314    Return a new HTML ID string.
2315    
2316    =over 4
2317    
2318    =item name
2319    
2320    Name to be prefixed to the ID string.
2321    
2322    =item RETURN
2323    
2324    Returns a hopefully-unique ID string.
2325    
2326    =back
2327    
2328    =cut
2329    
2330    sub GetDivID {
2331        # Get the parameters.
2332        my ($name) = @_;
2333        # Compute the ID.
2334        my $retVal = "elt_$name$divCount";
2335        # Increment the counter to make sure this ID is not re-used.
2336        $divCount++;
2337        # Return the result.
2338        return $retVal;
2339    }
2340    
2341  =head2 Feature Column Methods  =head2 Feature Column Methods
2342    
2343  The methods in this column manage feature column data. If you want to provide the  The methods in this section manage feature column data. If you want to provide the
2344  capability to include new types of data in feature columns, then all the changes  capability to include new types of data in feature columns, then all the changes
2345  are made to this section of the source file. Technically, this should be implemented  are made to this section of the source file. Technically, this should be implemented
2346  using object-oriented methods, but this is simpler for non-programmers to maintain.  using object-oriented methods, but this is simpler for non-programmers to maintain.
# Line 1657  Line 2348 
2348  the name for the protein page link column is C<protlink>. If the column is to appear  the name for the protein page link column is C<protlink>. If the column is to appear
2349  in the default list of feature columns, add it to the list returned by  in the default list of feature columns, add it to the list returned by
2350  L</DefaultFeatureColumns>. Then add code to produce the column title to  L</DefaultFeatureColumns>. Then add code to produce the column title to
2351  L</FeatureColumnTitle> and code to produce its value to L</FeatureColumnValue>, and  L</FeatureColumnTitle> and code to produce its value to L</FeatureColumnValue>. If the
2352  everything else will happen automatically.  feature column should be excluded from downloads, add it to the C<FeatureColumnSkip>
2353    hash. Everything else will happen automatically.
2354    
2355  There is one special column name syntax for extra columns (that is, nonstandard  There is a special column name syntax for extra columns (that is, nonstandard
2356  feature columns). If the column name begins with C<X=>, then it is presumed to be  feature columns). If the column name begins with C<X=>, then it is presumed to be
2357  an extra column. The column title is the text after the C<X=>, and its value is  an extra column. The column title is the text after the C<X=>, and its value is
2358  pulled from the extra column hash.  pulled from the extra column hash.
2359    
2360    =cut
2361    
2362    # This hash is used to determine which columns should not be included in downloads.
2363    my %FeatureColumnSkip = map { $_ => 1 } qw(gblink viewerlink protlink);
2364    
2365  =head3 DefaultFeatureColumns  =head3 DefaultFeatureColumns
2366    
2367  C<< my $colNames = $shelp->DefaultFeatureColumns(); >>  C<< my @colNames = $shelp->DefaultFeatureColumns(); >>
2368    
2369  Return a reference to a list of the default feature column identifiers. These  Return a list of the default feature column identifiers. These identifiers can
2370  identifiers can be passed to L</FeatureColumnTitle> and L</FeatureColumnValue> in  be passed to L</FeatureColumnTitle> and L</FeatureColumnValue> in order to
2371  order to produce the column titles and row values.  produce the column titles and row values.
2372    
2373  =cut  =cut
2374    
# Line 1679  Line 2376 
2376      # Get the parameters.      # Get the parameters.
2377      my ($self) = @_;      my ($self) = @_;
2378      # Return the result.      # Return the result.
2379      return ['orgName', 'function', 'gblink', 'protlink',      return qw(orgName function gblink protlink);
             FeatureQuery::AdditionalColumns($self)];  
2380  }  }
2381    
2382  =head3 FeatureColumnTitle  =head3 FeatureColumnTitle
# Line 1712  Line 2408 
2408      if ($colName =~ /^X=(.+)$/) {      if ($colName =~ /^X=(.+)$/) {
2409          # Here we have an extra column.          # Here we have an extra column.
2410          $retVal = $1;          $retVal = $1;
     } elsif ($colName eq 'orgName') {  
         $retVal = "Name";  
     } elsif ($colName eq 'fid') {  
         $retVal = "FIG ID";  
2411      } elsif ($colName eq 'alias') {      } elsif ($colName eq 'alias') {
2412          $retVal = "External Aliases";          $retVal = "External Aliases";
2413        } elsif ($colName eq 'fid') {
2414            $retVal = "FIG ID";
2415      } elsif ($colName eq 'function') {      } elsif ($colName eq 'function') {
2416          $retVal = "Functional Assignment";          $retVal = "Functional Assignment";
2417      } elsif ($colName eq 'gblink') {      } elsif ($colName eq 'gblink') {
2418          $retVal = "GBrowse";          $retVal = "GBrowse";
     } elsif ($colName eq 'protlink') {  
         $retVal = "NMPDR Protein Page";  
2419      } elsif ($colName eq 'group') {      } elsif ($colName eq 'group') {
2420          $retVal = "NMDPR Group";          $retVal = "NMDPR Group";
2421        } elsif ($colName =~ /^keyword:(.+)$/) {
2422            $retVal = ucfirst $1;
2423        } elsif ($colName eq 'orgName') {
2424            $retVal = "Organism and Gene ID";
2425        } elsif ($colName eq 'protlink') {
2426            $retVal = "NMPDR Protein Page";
2427        } elsif ($colName eq 'viewerlink') {
2428            $retVal = "Annotation Page";
2429        } elsif ($colName eq 'subsystem') {
2430            $retVal = "Subsystems";
2431      }      }
2432      # Return the result.      # Return the result.
2433      return $retVal;      return $retVal;
2434  }  }
2435    
2436    =head3 FeatureColumnDownload
2437    
2438    C<< my $keep = $shelp->FeatureColumnDownload($colName); >>
2439    
2440    Return TRUE if the named feature column is to be kept when downloading, else FALSE.
2441    
2442    =over 4
2443    
2444    =item colName
2445    
2446    Name of the relevant feature column.
2447    
2448    =item RETURN
2449    
2450    Return TRUE if the named column should be kept while downloading, else FALSE. In general,
2451    FALSE is returned if the column generates a button, image, or other purely-HTML value.
2452    
2453    =back
2454    
2455    =cut
2456    
2457    sub FeatureColumnDownload {
2458        # Get the parameters.
2459        my ($self, $colName) = @_;
2460        # Return the determination. We download the column if it's not in the skip-hash.
2461        # Note we return 0 and 1 instead of 1 and undef because it simplifies some tracing.
2462        return (exists $FeatureColumnSkip{$colName} ? 0 : 1);
2463    }
2464    
2465    
2466  =head3 FeatureColumnValue  =head3 FeatureColumnValue
2467    
2468  C<< my $value = $shelp->FeatureColumnValue($colName, $fid, \%extraCols); >>  C<< my $value = $shelp->FeatureColumnValue($colName, $fid, \%extraCols); >>
# Line 1745  Line 2477 
2477    
2478  =item record  =item record
2479    
2480  DBObject record for the feature being displayed in the current row.  ERDBObject record for the feature being displayed in the current row.
2481    
2482  =item extraCols  =item extraCols
2483    
# Line 1781  Line 2513 
2513          if (defined $extraCols->{$1}) {          if (defined $extraCols->{$1}) {
2514              $retVal = $extraCols->{$1};              $retVal = $extraCols->{$1};
2515          }          }
     } elsif ($colName eq 'orgName') {  
         # Here we want the formatted organism name and feature number.  
         $retVal = $self->FeatureName($fid);  
     } elsif ($colName eq 'fid') {  
         # Here we have the raw feature ID. We hyperlink it to the protein page.  
         $retVal = HTML::set_prot_links($fid);  
2516      } elsif ($colName eq 'alias') {      } elsif ($colName eq 'alias') {
2517          # In this case, the user wants a list of external aliases for the feature.          # In this case, the user wants a list of external aliases for the feature.
2518          # These are very expensive, so we compute them when the row is displayed.          # These are very expensive, so we compute them when the row is displayed.
2519          $retVal = "%%aliases=$fid";          # To do the computation, we need to know the favored alias type and the
2520            # feature ID.
2521            my $favored = $cgi->param("FavoredAlias") || "fig";
2522            $retVal = "%%alias=$fid,$favored";
2523        } elsif ($colName eq 'fid') {
2524            # Here we have the raw feature ID. We hyperlink it to the protein page.
2525            $retVal = HTML::set_prot_links($fid);
2526      } elsif ($colName eq 'function') {      } elsif ($colName eq 'function') {
2527          # The functional assignment is just a matter of getting some text.          # The functional assignment is just a matter of getting some text.
2528          ($retVal) = $record->Value('Feature(assignment)');          ($retVal) = $record->Value('Feature(assignment)');
2529      } elsif ($colName eq 'gblink') {      } elsif ($colName eq 'gblink') {
2530          # Here we want a link to the GBrowse page using the official GBrowse button.          # Here we want a link to the GBrowse page using the official GBrowse button.
2531          my $gurl = "GetGBrowse.cgi?fid=$fid";          $retVal = FakeButton('GBrowse', "GetGBrowse.cgi", undef,
2532          $retVal = $cgi->a({ href => $gurl, title => "GBrowse for $fid" },                            fid => $fid);
                           $cgi->img({ src => "../images/button-gbrowse.png",  
                                       border => 0 })  
                          );  
     } elsif ($colName eq 'protlink') {  
         # Here we want a link to the protein page using the official NMPDR button.  
         my $hurl = HTML::fid_link($cgi, $fid, 0, 1);  
         $retVal = $cgi->a({ href => $hurl, title => "Protein page for $fid" },  
                           $cgi->img({ src => "../images/button-nmpdr.png",  
                                      border => 0 })  
                          );  
2533      } elsif ($colName eq 'group') {      } elsif ($colName eq 'group') {
2534          # Get the NMPDR group name.          # Get the NMPDR group name.
2535          my (undef, $group) = $self->OrganismData($fid);          my (undef, $group) = $self->OrganismData($fid);
# Line 1815  Line 2537 
2537          my $nurl = $sprout->GroupPageName($group);          my $nurl = $sprout->GroupPageName($group);
2538          $retVal = $cgi->a({ href => $nurl, title => "$group summary" },          $retVal = $cgi->a({ href => $nurl, title => "$group summary" },
2539                            $group);                            $group);
2540        } elsif ($colName =~ /^keyword:(.+)$/) {
2541            # Here we want keyword-related values. This is also expensive, so
2542            # we compute them when the row is displayed.
2543            $retVal = "%%$colName=$fid";
2544        } elsif ($colName eq 'orgName') {
2545            # Here we want the formatted organism name and feature number.
2546            $retVal = $self->FeatureName($fid);
2547        } elsif ($colName eq 'protlink') {
2548            # Here we want a link to the protein page using the official NMPDR button.
2549            $retVal = FakeButton('NMPDR', "protein.cgi", undef,
2550                              prot => $fid, SPROUT => 1, new_framework => 0,
2551                              user => '');
2552        } elsif ($colName eq 'viewerlink') {
2553            # Here we want a link to the SEED viewer page using the official viewer button.
2554            $retVal = FakeButton('Annotation', "index.cgi", undef,
2555                                 action => 'ShowAnnotation', prot => $fid);
2556        } elsif ($colName eq 'subsystem') {
2557            # Another run-time column: subsystem list.
2558            $retVal = "%%subsystem=$fid";
2559      }      }
2560      # Return the result.      # Return the result.
2561      return $retVal;      return $retVal;
# Line 1853  Line 2594 
2594      # Get the Sprout and CGI objects.      # Get the Sprout and CGI objects.
2595      my $sprout = $self->DB();      my $sprout = $self->DB();
2596      my $cgi = $self->Q();      my $cgi = $self->Q();
2597        Trace("Runtime column $type with text \"$text\" found.") if T(4);
2598      # Separate the text into a type and data.      # Separate the text into a type and data.
2599      if ($type eq 'aliases') {      if ($type eq 'alias') {
2600          # Here the caller wants external alias links for a feature. The text          # Here the caller wants external alias links for a feature. The text
2601          # is the feature ID.          # parameter for computing the alias is the feature ID followed by
2602          my $fid = $text;          # the favored alias type.
2603          # The complicated part is we have to hyperlink them. First, get the          my ($fid, $favored) = split /\s*,\s*/, $text;
2604          # aliases.          # The complicated part is we have to hyperlink them and handle the
2605            # favorites. First, get the aliases.
2606          Trace("Generating aliases for feature $fid.") if T(4);          Trace("Generating aliases for feature $fid.") if T(4);
2607          my @aliases = $sprout->FeatureAliases($fid);          my @aliases = sort $sprout->FeatureAliases($fid);
2608          # Only proceed if we found some.          # Only proceed if we found some.
2609          if (@aliases) {          if (@aliases) {
2610              # Join the aliases into a comma-delimited list.              # Split the aliases into favored and unfavored.
2611              my $aliasList = join(", ", @aliases);              my @favored = ();
2612                my @unfavored = ();
2613                for my $alias (@aliases) {
2614                    # Use substr instead of pattern match because $favored is specified by the user
2615                    # and we don't want him to put funny meta-characters in there.
2616                    if (substr($alias, 0, length($favored)) eq $favored) {
2617                        push @favored, $alias;
2618                    } else {
2619                        push @unfavored, $alias;
2620                    }
2621                }
2622                # Rejoin the aliases into a comma-delimited list, with the favored ones first.
2623                my $aliasList = join(", ", @favored, @unfavored);
2624              # Ask the HTML processor to hyperlink them.              # Ask the HTML processor to hyperlink them.
2625              $retVal = HTML::set_prot_links($cgi, $aliasList);              $retVal = HTML::set_prot_links($cgi, $aliasList);
2626          }          }
2627        } elsif ($type eq 'subsystem') {
2628            # Here the caller wants the subsystems in which this feature participates.
2629            # The text is the feature ID. We will list the subsystem names with links
2630            # to the subsystem's summary page.
2631            my $fid = $text;
2632            # Get the subsystems.
2633            Trace("Generating subsystems for feature $fid.") if T(4);
2634            my %subs = $sprout->SubsystemsOf($fid);
2635            # Extract the subsystem names.
2636            my @names = map { HTML::sub_link($cgi, $_) } sort keys %subs;
2637            # String them into a list.
2638            $retVal = join(", ", @names);
2639        } elsif ($type =~ /^keyword:(.+)$/) {
2640            # Here the caller wants the value of the named keyword. The text is the
2641            # feature ID.
2642            my $keywordName = $1;
2643            my $fid = $text;
2644            # Get the attribute values.
2645            Trace("Getting $keywordName values for feature $fid.") if T(4);
2646            my @values = $sprout->GetFlat(['Feature'], "Feature(id) = ?", [$fid],
2647                                          "Feature($keywordName)");
2648            # String them into a list.
2649            $retVal = join(", ", @values);
2650        }
2651        # Return the result.
2652        return $retVal;
2653    }
2654    
2655    =head3 SaveOrganismData
2656    
2657    C<< my ($name, $displayGroup) = $shelp->SaveOrganismData($group, $genomeID, $genus, $species, $strain); >>
2658    
2659    Format the name of an organism and the display version of its group name. The incoming
2660    data should be the relevant fields from the B<Genome> record in the database. The
2661    data will also be stored in the genome cache for later use in posting search results.
2662    
2663    =over 4
2664    
2665    =item group
2666    
2667    Name of the genome's group as it appears in the database.
2668    
2669    =item genomeID
2670    
2671    ID of the relevant genome.
2672    
2673    =item genus
2674    
2675    Genus of the genome's organism. If undefined or null, it will be assumed the genome is not
2676    in the database. In this case, the organism name is derived from the genomeID and the group
2677    is automatically the supporting-genomes group.
2678    
2679    =item species
2680    
2681    Species of the genome's organism.
2682    
2683    =item strain
2684    
2685    Strain of the species represented by the genome.
2686    
2687    =item RETURN
2688    
2689    Returns a two-element list. The first element is the formatted genome name. The second
2690    element is the display name of the genome's group.
2691    
2692    =back
2693    
2694    =cut
2695    
2696    sub SaveOrganismData {
2697        # Get the parameters.
2698        my ($self, $group, $genomeID, $genus, $species, $strain) = @_;
2699        # Declare the return values.
2700        my ($name, $displayGroup);
2701        # If the organism does not exist, format an unknown name and a blank group.
2702        if (! defined($genus)) {
2703            $name = "Unknown Genome $genomeID";
2704            $displayGroup = "";
2705        } else {
2706            # It does exist, so format the organism name.
2707            $name = "$genus $species";
2708            if ($strain) {
2709                $name .= " $strain";
2710            }
2711            # Compute the display group. This is currently the same as the incoming group
2712            # name unless it's the supporting group, which is nulled out.
2713            $displayGroup = ($group eq $FIG_Config::otherGroup ? "" : $group);
2714        }
2715        # Cache the group and organism data.
2716        my $cache = $self->{orgs};
2717        $cache->{$genomeID} = [$name, $displayGroup];
2718        # Return the result.
2719        return ($name, $displayGroup);
2720    }
2721    
2722    =head3 ValidateKeywords
2723    
2724    C<< my $okFlag = $shelp->ValidateKeywords($keywordString, $required); >>
2725    
2726    Insure that a keyword string is reasonably valid. If it is invalid, a message will be
2727    set.
2728    
2729    =over 4
2730    
2731    =item keywordString
2732    
2733    Keyword string specified as a parameter to the current search.
2734    
2735    =item required
2736    
2737    TRUE if there must be at least one keyword specified, else FALSE.
2738    
2739    =item RETURN
2740    
2741    Returns TRUE if the keyword string is valid, else FALSE. Note that a null keyword string
2742    is acceptable if the I<$required> parameter is not specified.
2743    
2744    =back
2745    
2746    =cut
2747    
2748    sub ValidateKeywords {
2749        # Get the parameters.
2750        my ($self, $keywordString, $required) = @_;
2751        # Declare the return variable.
2752        my $retVal = 0;
2753        my @wordList = split /\s+/, $keywordString;
2754        # Right now our only real worry is a list of all minus words. The problem with it is that
2755        # it will return an incorrect result.
2756        my @plusWords = grep { $_ =~ /^[^\-]/ } @wordList;
2757        if (! @wordList) {
2758            if ($required) {
2759                $self->SetMessage("No search words specified.");
2760            } else {
2761                $retVal = 1;
2762            }
2763        } elsif (! @plusWords) {
2764            $self->SetMessage("At least one keyword must be positive. All the keywords entered are preceded by minus signs.");
2765        } else {
2766            $retVal = 1;
2767        }
2768        # Return the result.
2769        return $retVal;
2770    }
2771    
2772    =head3 FakeButton
2773    
2774    C<< my $html = SearchHelper::FakeButton($caption, $url, $target, %parms); >>
2775    
2776    Create a fake button that hyperlinks to the specified URL with the specified parameters.
2777    Unlike a real button, this one won't visibly click, but it will take the user to the
2778    correct place.
2779    
2780    The parameters of this method are deliberately identical to L</Formlet> so that we
2781    can switch easily from real buttons to fake ones in the code.
2782    
2783    =over 4
2784    
2785    =item caption
2786    
2787    Caption to be put on the button.
2788    
2789    =item url
2790    
2791    URL for the target page or script.
2792    
2793    =item target
2794    
2795    Frame or target in which the new page should appear. If C<undef> is specified,
2796    the default target will be used.
2797    
2798    =item parms
2799    
2800    Hash containing the parameter names as keys and the parameter values as values.
2801    These will be appended to the URL.
2802    
2803    =back
2804    
2805    =cut
2806    
2807    sub FakeButton {
2808        # Get the parameters.
2809        my ($caption, $url, $target, %parms) = @_;
2810        # Declare the return variable.
2811        my $retVal;
2812        # Compute the target URL.
2813        my $targetUrl = "$url?" . join(";", map { "$_=" . uri_escape($parms{$_}) } keys %parms);
2814        # Compute the target-frame HTML.
2815        my $targetHtml = ($target ? " target=\"$target\"" : "");
2816        # Assemble the result.
2817        return "<a href=\"$targetUrl\" $targetHtml><div class=\"button2 button\">$caption</div></a>";
2818    }
2819    
2820    =head3 Formlet
2821    
2822    C<< my $html = SearchHelper::Formlet($caption, $url, $target, %parms); >>
2823    
2824    Create a mini-form that posts to the specified URL with the specified parameters. The
2825    parameters will be stored in hidden fields, and the form's only visible control will
2826    be a submit button with the specified caption.
2827    
2828    Note that we don't use B<CGI.pm> services here because they generate forms with extra characters
2829    and tags that we don't want to deal with.
2830    
2831    =over 4
2832    
2833    =item caption
2834    
2835    Caption to be put on the form button.
2836    
2837    =item url
2838    
2839    URL to be put in the form's action parameter.
2840    
2841    =item target
2842    
2843    Frame or target in which the form results should appear. If C<undef> is specified,
2844    the default target will be used.
2845    
2846    =item parms
2847    
2848    Hash containing the parameter names as keys and the parameter values as values.
2849    
2850    =back
2851    
2852    =cut
2853    
2854    sub Formlet {
2855        # Get the parameters.
2856        my ($caption, $url, $target, %parms) = @_;
2857        # Compute the target HTML.
2858        my $targetHtml = ($target ? " target=\"$target\"" : "");
2859        # Start the form.
2860        my $retVal = "<form method=\"POST\" action=\"$url\"$target>";
2861        # Add the parameters.
2862        for my $parm (keys %parms) {
2863            $retVal .= "<input type=\"hidden\" name=\"$parm\" value=\"$parms{$parm}\" />";
2864        }
2865        # Put in the button.
2866        $retVal .= "<input type=\"submit\" name=\"submit\" value=\"$caption\" class=\"button\" />";
2867        # Close the form.
2868        $retVal .= "</form>";
2869        # Return the result.
2870        return $retVal;
2871    }
2872    
2873    =head3 TuningParameters
2874    
2875    C<< my $options = $shelp->TuningParameters(%parmHash); >>
2876    
2877    Retrieve tuning parameters from the CGI query object. The parameter is a hash that maps parameter names
2878    to their default values. The parameters and their values will be returned as a hash reference.
2879    
2880    =over 4
2881    
2882    =item parmHash
2883    
2884    Hash mapping parameter names to their default values.
2885    
2886    =item RETURN
2887    
2888    Returns a reference to a hash containing the parameter names mapped to their actual values.
2889    
2890    =back
2891    
2892    =cut
2893    
2894    sub TuningParameters {
2895        # Get the parameters.
2896        my ($self, %parmHash) = @_;
2897        # Declare the return variable.
2898        my $retVal = {};
2899        # Get the CGI Query Object.
2900        my $cgi = $self->Q();
2901        # Loop through the parameter names.
2902        for my $parm (keys %parmHash) {
2903            # Get the incoming value for this parameter.
2904            my $value = $cgi->param($parm);
2905            # Zero might be a valid value, so we do an is-defined check rather than an OR.
2906            if (defined($value)) {
2907                $retVal->{$parm} = $value;
2908            } else {
2909                $retVal->{$parm} = $parmHash{$parm};
2910            }
2911      }      }
2912      # Return the result.      # Return the result.
2913      return $retVal;      return $retVal;
# Line 1901  Line 2940 
2940    
2941  =head3 SortKey  =head3 SortKey
2942    
2943  C<< my $key = $shelp->SortKey($record); >>  C<< my $key = $shelp->SortKey($fdata); >>
2944    
2945  Return the sort key for the specified record. The default is to sort by feature name,  Return the sort key for the specified feature data. The default is to sort by feature name,
2946  floating NMPDR organisms to the top. This sort may be overridden by the search class  floating NMPDR organisms to the top. If a full-text search is used, then the default
2947  to provide fancier functionality. This method is called by B<PutFeature>, so it  sort is by relevance followed by feature name. This sort may be overridden by the
2948  is only used for feature searches. A non-feature search would presumably have its  search class to provide fancier functionality. This method is called by
2949  own sort logic.  B<PutFeature>, so it is only used for feature searches. A non-feature search
2950    would presumably have its own sort logic.
2951    
2952  =over 4  =over 4
2953    
2954  =item record  =item record
2955    
2956  The C<DBObject> from which the current row of data is derived.  The C<FeatureData> containing the current feature.
2957    
2958  =item RETURN  =item RETURN
2959    
# Line 1925  Line 2965 
2965    
2966  sub SortKey {  sub SortKey {
2967      # Get the parameters.      # Get the parameters.
2968      my ($self, $record) = @_;      my ($self, $fdata) = @_;
2969      # Get the feature ID from the record.      # Get the feature ID from the record.
2970      my ($fid) = $record->Value('Feature(id)');      my $fid = $fdata->FID();
2971      # Get the group from the feature ID.      # Get the group from the feature ID.
2972      my $group = $self->FeatureGroup($fid);      my $group = $self->FeatureGroup($fid);
2973      # Ask the feature query object to form the sort key.      # Ask the feature query object to form the sort key.
2974      my $retVal = FeatureQuery::SortKey($self, $group, $record);      my $retVal = $fdata->SortKey($self, $group);
2975      # Return the result.      # Return the result.
2976      return $retVal;      return $retVal;
2977  }  }
2978    
2979    =head3 PrintLine
2980    
2981    C<< $shelp->PrintLine($message); >>
2982    
2983    Print a line of CGI output. This is used during the operation of the B<Find> method while
2984    searching, so the user sees progress in real-time.
2985    
2986    =over 4
2987    
2988    =item message
2989    
2990    HTML text to display.
2991    
2992    =back
2993    
2994    =cut
2995    
2996    sub PrintLine {
2997        # Get the parameters.
2998        my ($self, $message) = @_;
2999        # Send them to the output.
3000        print "$message\n";
3001    }
3002    
3003    
3004  1;  1;

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